scholarly journals An update of molecular pathology of bone tumors. Lessons learned from investigating samples by next generation sequencing

2018 ◽  
Vol 58 (2) ◽  
pp. 88-99 ◽  
Author(s):  
Daniel Baumhoer ◽  
Fernanda Amary ◽  
Adrienne M. Flanagan
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Pathology ◽  
Bone Tumors ◽  
Lessons Learned ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Designing Myeloid Gene Panels

2021 ◽  
Author(s):  
Fang Zhao ◽  
David S. Bosler ◽  
James R. Cook
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Pathology ◽  
Diagnostic Yield ◽  
Gene Panel ◽  
Next Generation ◽  
Gene Set ◽  
Variants Of Unknown Significance ◽  
The Core ◽  
Unknown Significance ◽  
Generation Sequencing

Context.— Next-generation sequencing studies are increasingly used in the evaluation of suspected chronic myeloid neoplasms (CMNs), but there is wide variability among laboratories in the genes analyzed for this purpose. Recently, the Association for Molecular Pathology CMN working group recommended a core 34-gene set as a minimum target list for evaluation of CMNs. This list was recommended based on literature review, and its diagnostic yield in clinical practice is unknown. Objective.— To determine the diagnostic yield of the core 34 genes and assess the potential impact of including selected additional genes. Design.— We retrospectively reviewed 185 patients with known or suspected CMNs tested using a 62-gene next-generation sequencing panel that included all 34 core genes. Results.— The Association for Molecular Pathology's core 34 genes had a diagnostic yield of 158 of 185 (85.4%) to detect at least 1 variant with strong/potential clinical significance and 107 of 185 (57.8%) to detect at least 2 such variants. The 62-gene panel had a diagnostic yield of 160 of 185 (86.5%) and 112 of 185 (60.5%), respectively. Variants of unknown significance were identified in 49 of 185 (26.5%) using the core 34 genes versus 76 of 185 (41.1%) using the 62-gene panel. Conclusions.— This study demonstrates that the Association for Molecular Pathology–recommended core 34-gene set has a high diagnostic yield in CMNs. Inclusion of selected additional genes slightly increases the rate of abnormal results, while also increasing the detection of variants of unknown significance. We recommend inclusion of CUX1, DDX41, ETNK1, RIT1, and SUZ12 in addition to the Association for Molecular Pathology's 34-gene core set for routine evaluation of CMNs.

Oncogenic viruses: Lessons learned using next-generation sequencing technologies

2016 ◽  
Vol 61 ◽  
pp. 61-68 ◽  
Author(s):  
Ronan Flippot ◽  
Gabriel G. Malouf ◽  
Xiaoping Su ◽  
David Khayat ◽  
Jean-Philippe Spano
Keyword(s):  
Next Generation Sequencing ◽  
Lessons Learned ◽  
Oncogenic Viruses ◽  
Next Generation ◽  
Sequencing Technologies ◽  
Generation Sequencing

scholarly journals In vivo optical imaging-guided targeted sampling for precise diagnosis and molecular pathology

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aditi Sahu ◽  
Yuna Oh ◽  
Gary Peterson ◽  
Miguel Cordova ◽  
Cristian Navarrete-Dechent ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Pathology ◽  
Ex Vivo ◽  
Molecular Profiling ◽  
Next Generation ◽  
Spatial Targeting ◽  
Mutational Profiling ◽  
Generation Sequencing

AbstractConventional tissue sampling can lead to misdiagnoses and repeated biopsies. Additionally, tissue processed for histopathology suffers from poor nucleic acid quality and/or quantity for downstream molecular profiling. Targeted micro-sampling of tissue can ensure accurate diagnosis and molecular profiling in the presence of spatial heterogeneity, especially in tumors, and facilitate acquisition of fresh tissue for molecular analysis. In this study, we explored the feasibility of performing 1–2 mm precision biopsies guided by high-resolution reflectance confocal microscopy (RCM) and optical coherence tomography (OCT), and reflective metallic grids for accurate spatial targeting. Accurate sampling was confirmed with either histopathology or molecular profiling through next generation sequencing (NGS) in 9 skin cancers in 7 patients. Imaging-guided 1–2 mm biopsies enabled spatial targeting for in vivo diagnosis, feature correlation and depth assessment, which were confirmed with histopathology. In vivo 1-mm targeted biopsies achieved adequate quantity and high quality of DNA for next-generation sequencing. Subsequent mutational profiling was confirmed on 1 melanoma in situ and 2 invasive melanomas, using a 505-gene mutational panel called Memorial Sloan Kettering-Integrated mutational profiling of actionable cancer targets (MSK-IMPACT). Differential mutational landscapes, in terms of number and types of mutations, were found between invasive and in situ melanomas in a single patient. Our findings demonstrate feasibility of accurate sampling of regions of interest for downstream histopathological diagnoses and molecular pathology in both in vivo and ex vivo settings with broad diagnostic, therapeutic and research potential in cutaneous diseases accessible by RCM-OCT imaging.

Sign in / Sign up

Export Citation Format

Share Document